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Irregularly sampled multivariate event streams remain a stubbornly difficult modality for generative modeling: tokenization-based approaches break down when inter-event intervals vary by orders of magnitude, and neural temporal point…
We present a browser application for estimating the number of frequent patterns, in particular itemsets, as well as the pattern frequency spectrum. The pattern frequency spectrum is defined as the function that shows for every value of the…
Time-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function…
We reconsider the deterministic haploid mutation-selection equation with two types. This is an ordinary differential equation that describes the type distribution (forward in time) in a population of infinite size. This paper establishes…
Recovery of population size history from molecular sequence data is an important problem in population genetics. Inference commonly relies on a coalescent model linking the population size history to genealogies. The high computational cost…
Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population…
A simple analytical framework to study the molecular quasispecies evolution of finite populations is proposed, in which the population is assumed to be a random combination of the constiyuent molecules in each generation,i.e., linkage…
Aims: To propose a general sample size framework for developing or updating a clinical prediction model using any statistical or machine learning method, based on drawing samples from anticipated posterior distributions and targeting…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
In uses of pre-trained machine learning models, it is a known issue that the target population in which the model is being deployed may not have been reflected in the source population with which the model was trained. This can result in a…
We introduce a modified spatial $\Lambda$-Fleming-Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective…
We introduce a general diploid population model with self-fertilization and possible overlapping generations, and study the genealogy of a sample of $n$ genes as the population size $N$ tends to infinity. Unlike traditional approach in…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
The multivariate hypergeometric distribution describes sampling without replacement from a discrete population of elements divided into multiple categories. Addressing a gap in the literature, we tackle the challenge of estimating discrete…
We propose a change-point detection method for large scale multiple testing problems with data having clustered signals. Unlike the classic change-point setup, the signals can vary in size within a cluster. The clustering structure on the…
A forward diffusion equation describing the evolution of the allele frequency spectrum is presented. The influx of mutations is accounted for by imposing a suitable boundary condition. For a Wright-Fisher diffusion with or without selection…
We revisit the classical population genetics model of a population evolving under multiplicative selection, mutation and drift. The number of beneficial alleles in a multi-locus system can be considered a trait under exponential selection.…
Reconstructing past population size from present day genetic data is a major goal of population genetics. Recent empirical studies infer population size history using coalescent-based models applied to a small number of individuals. Here we…
Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…
Evolutionary models for populations of constant size are frequently studied using the Moran model, the Wright-Fisher model, or their diffusion limits. When evolution is neutral, a random genealogy given through Kingman's coalescent is used…